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chr1    100    159    0
chr1    200    260    0
...
chr11    679    687    0
chr24    100    200    0
chr24    300    400    0

chr1    104    104    0    0    +
chr1    145    145    0    0    +
...
chr24    105    105    0    0    +
chr24    110    110    0    0    +
chr24    350    350    0    0    +

#!/usr/bin/perl 
use warnings; use strict; 
...
close R;
close P;
close OUT;

chr1    100    159    0    104    104    0    0    +
chr1    100    159    0    145    145    0    0    +

chr1    100    159    0    chr1    104    104    0    0    +
chr1    100    159    0    chr1    145    145    0    0    +
...
chr22    100    200    0    chr22    105    105    0    0    +
chr22    100    200    0    chr22    110    110    0    0    +
chr22    300    400    0    chr22    350    350    0    0    +